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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
NASA NTRS1988

Quantum mechanical algebraic variational methods for inelastic and reactive molecular collisions

The quantum mechanical problem of reactive or nonreactive scattering of atoms and molecules is formulated in terms of square-integrable basis sets with variational expressions for the reactance matrix. Several formulations involving expansions of the wave function (the Schwinger variational principle) or amplitude density (a generalization of the Newton variational principle), single-channel or multichannel distortion potentials, and primitive or contracted basis functions are presented and tested. The test results, for inelastic and reactive atom-diatom collisions, suggest that the methods may be useful for a variety of collision calculations and may allow the accurate quantal treatment of systems for which other available methods would be prohibitively expensive.

Schwenke, David W.↗
DOE OSTI2025

Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry

Fragment-based quantum chemistry methods offer a way to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation to compute protein–ligand interaction energies in systems with several thousand atoms, using a new software platform for managing fragment-based calculations that implements a screened many-body expansion. Convergence tests using a minimal-basis semiempirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to within 1 kcal/mol at about 1% of the computational cost. We also demonstrate that the HF-3c results are illustrative of trends obtained with density functional theory in basis sets up to augmented quadruple-ζ quality. Strategic deployment of fragmentation facilitates the use of converged biomolecular model systems alongside high-quality electronic structure methods and basis sets, bringing ab initio quantum chemistry to systems of hitherto unimaginable size. This will be useful for generation of high-quality training data for machine learning applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Dirac cones in the spectrum of bond-decorated graphenes

We present a two-band model based on periodic Hückel theory, which is capable of predicting the existence and position of Dirac cones in the first Brillouin zone of an infinite class of two-dimensional periodic carbon networks, obtained by systematic perturbation of the graphene connectivity by bond decoration, that is by inclusion of arbitrary π-electron Hückel networks into each of the three carbon–carbon π-bonds within the graphene unit cell. The bond decoration process can fundamentally modify the graphene unit cell and honeycomb connectivity, representing a simple and general way to describe many cases of graphene chemical functionalization of experimental interest, such as graphyne, janusgraphenes, and chlorographenes. Exact mathematical conditions for the presence of Dirac cones in the spectrum of the resulting two-dimensional π-networks are formulated in terms of the spectral properties of the decorating graphs. Our method predicts the existence of Dirac cones in experimentally characterized janusgraphenes and chlorographenes, recently speculated on the basis of density functional theory calculations. For these cases, our approach provides a proof of the existence of Dirac cones, and can be carried out at the cost of a back of the envelope calculation, bypassing any diagonalization step, even within Hückel theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Identification of early target genes of aflatoxin B1 in human hepatocytes, inter-individual variability and comparison with other genotoxic compounds

Gene expression profiling has recently emerged as a promising approach to identify early target genes and discriminate genotoxic carcinogens from non-genotoxic carcinogens and non-carcinogens. However, early gene changes induced by genotoxic compounds in human liver remain largely unknown. Primary human hepatocytes and differentiated HepaRG cells were exposed to aflatoxin B1 (AFB1) that induces DNA damage following enzyme-mediated bioactivation. Gene expression profile changes induced by a 24 h exposure of these hepatocyte models to 0.05 and 0.25 μM AFB1 were analyzed by using oligonucleotide pangenomic microarrays. The main altered signaling pathway was the p53 pathway and related functions such as cell cycle, apoptosis and DNA repair. Direct involvement of the p53 protein in response to AFB1 was verified by using siRNA directed against p53. Among the 83 well-annotated genes commonly modulated in two pools of three human hepatocyte populations and HepaRG cells, several genes were identified as altered by AFB1 for the first time. In addition, a subset of 10 AFB1-altered genes, selected upon basis of their function or tumor suppressor role, was tested in four human hepatocyte populations and in response to other chemicals. Although they exhibited large variable inter-donor fold-changes, several of these genes, particularly FHIT, BCAS3 and SMYD3, were found to be altered by various direct and other indirect genotoxic compounds and unaffected by non-genotoxic compounds. Overall, this comprehensive analysis of early gene expression changes induced by AFB1 in human hepatocytes identified a gene subset that included several genes representing potential biomarkers of genotoxic compounds. -- Highlights: ► Gene expression profile changes induced by aflatoxin B1 in human hepatocytes. ► AFB1 modulates various genes including tumor suppressor genes and proto-oncogenes. ► Important inter-individual variations in the response to AFB1. ► Some genes also altered by other genotoxic compounds requiring or not bioactivation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Robustness analysis of an air heating plant and control law by using polynomial chaos

This paper presents a robustness analysis of an air heating plant with a multivariable closed-loop control law by using the polynomial chaos methodology (MPC). The plant consists of a PVC tube with a fan in the air input (that forces the air through the tube) and a mass flux sensor in the output. A heating resistance warms the air as it flows inside the tube, and a thermo-couple sensor measures the air temperature. The plant has thus two inputs (the fan's rotation intensity and heat generated by the resistance, both measured in percent of the maximum value) and two outputs (air temperature and air mass flux, also in percent of the maximal value). The mathematical model is obtained by System Identification techniques. The mass flux sensor, which is nonlinear, is linearized and the delays in the transfer functions are properly approximated by non-minimum phase transfer functions. The resulting model is transformed to a state-space model, which is used for control design purposes. The multivariable robust control design techniques used is the LQG/LTR, and the controllers are validated in simulation software and in the real plant. Finally, the MPC is applied by considering some of the system's parameters as random variables (one at a time, and the system's stochastic differential equations are solved by expanding the solution (a stochastic process) in an orthogonal basis of polynomial functions of the basic random variables. This method transforms the stochastic equations in a set of deterministic differential equations, which can be solved by traditional numerical methods (That is the MPC). Statistical data for the system (like expected values and variances) are then calculated. The effects of randomness in the parameters are evaluated in the open-loop and closed-loop pole's positions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Knockdown of RMI1 impairs DNA repair under DNA replication stress

RMI1 (RecQ-mediated genome instability protein 1) forms a conserved BTR complex with BLM, Topo IIIα, and RMI2, and its absence causes genome instability. It has been revealed that RMI1 localizes to nuclear foci with BLM and Topo IIIα in response to replication stress, and that RMI1 functions downstream of BLM in promoting replication elongation. However, the precise functions of RMI1 during replication stress are not completely understood. Here we report that RMI1 knockdown cells are hypersensitive to hydroxyurea (HU). Using comet assay, we show that RMI1 knockdown cells exhibit accumulation of broken DNAs after being released from HU treatment. Moreover, we demonstrate that RMI1 facilitates the recovery from activated checkpoint and resuming the cell cycle after replicative stress. Surprisingly, loss of RMI1 results in a failure of RAD51 loading onto DNA damage sites. These findings reveal the importance of RMI1 in response to replication stress, which could explain the molecular basis for its function in maintaining genome integrity. - Highlights: • Knockdown of RMI1 enhances cell sensitivity to HU. • Knockdown of RMI1 accumulates excess broken DNAs after HU treatment. • Knockdown of RMI1 persists activated checkpoint after HU treatment. • RMI1 might facilitate the recruitment of RAD51 to damage sites.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1994

Development of New Open-Shell Perturbation and Coupled-Cluster Theories Based on Symmetric Spin Orbitals

A new spin orbital basis is employed in the development of efficient open-shell coupled-cluster and perturbation theories that are based on a restricted Hartree-Fock (RHF) reference function. The spin orbital basis differs from the standard one in the spin functions that are associated with the singly occupied spatial orbital. The occupied orbital (in the spin orbital basis) is assigned the delta(+) = 1/square root of 2(alpha+Beta) spin function while the unoccupied orbital is assigned the delta(-) = 1/square root of 2(alpha-Beta) spin function. The doubly occupied and unoccupied orbitals (in the reference function) are assigned the standard alpha and Beta spin functions. The coupled-cluster and perturbation theory wave functions based on this set of "symmetric spin orbitals" exhibit much more symmetry than those based on the standard spin orbital basis. This, together with interacting space arguments, leads to a dramatic reduction in the computational cost for both coupled-cluster and perturbation theory. Additionally, perturbation theory based on "symmetric spin orbitals" obeys Brillouin's theorem provided that spin and spatial excitations are both considered. Other properties of the coupled-cluster and perturbation theory wave functions and models will be discussed.

Lee, Timothy J.↗
DOE OSTI2016

Combined theoretical and experimental study of the valence, Rydberg, and ionic states of chlorobenzene

New photoelectron (PE) and ultra violet (UV) and vacuum UV (VUV) spectra have been obtained for chlorobenzene by synchrotron study with higher sensitivity and resolution than previous work and are subjected to detailed analysis. In addition, we report on the mass-resolved (2 + 1) resonance enhanced multiphoton ionization (REMPI) spectra of a jet-cooled sample. Both the VUV and REMPI spectra have enabled identification of a considerable number of Rydberg states for the first time. The use of ab initio calculations, which include both multi-reference multi-root doubles and singles configuration interaction (MRD-CI) and time dependent density functional theoretical (TDDFT) methods, has led to major advances in interpretation of the vibrational structure of the ionic and electronically excited states. Franck-Condon (FC) analyses of the PE spectra, including both hot and cold bands, indicate much more complex envelopes than previously thought. The sequence of ionic states can be best interpreted by our multi-configuration self-consistent field computations and also by comparison of the calculated vibrational structure of the B and C ionic states with experiment; these conclusions suggest that the leading sequence is the same as that of iodobenzene and bromobenzene, namely: X{sup 2}B{sub 1}(3b{sub 1}{sup −1}) < A{sup 2}A{sub 2}(1a{sub 2}{sup −1}) < B{sup 2}B{sub 2}(6b{sub 2}{sup −1}) < C{sup 2}B{sub 1}(2b{sub 1}{sup −1}). The absorption onset near 4.6 eV has been investigated using MRD-CI and TDDFT calculations; the principal component of this band is {sup 1}B{sub 2} and an interpretation based on the superposition of FC and Herzberg-Teller contributions has been performed. The other low-lying absorption band near 5.8 eV is dominated by a {sup 1}A{sub 1} state, but an underlying weak {sup 1}B{sub 1} state (πσ{sup ∗}) is also found. The strongest band in the VUV spectrum near 6.7 eV is poorly resolved and is analyzed in terms of two ππ{sup ∗} states of {sup 1}A{sub 1} (higher oscillator strength) and {sup 1}B{sub 2} (lower oscillator strength) symmetries, respectively. The calculated vertical excitation energies of these two states are critically dependent upon the presence of Rydberg functions in the basis set, since both manifolds are strongly perturbed by the Rydberg states in this energy range. A number of equilibrium structures of the ionic and singlet excited states show that the molecular structure is less subject to variation than corresponding studies for iodobenzene and bromobenzene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Crystal-momentum-resolved contributions to high-order harmonic generation in solids

We analytically and numerically investigate the emission of high-order harmonic radiation from model solids by intense few-cycle midinfrared laser pulses. In single-active-electron approximation, we expand the active electron's wave function in a basis of adiabatic Houston states and describe the solid's electronic band structure in terms of an adjustable Kronig-Penney model potential. For high-order harmonic generation (HHG) from MgO crystals, we examine spectra from two-band and converged multiband numerical calculations. We discuss the characteristics of intra- and interband contributions to the HHG spectrum for computations including initial crystal momenta either from the Γ point at the center of the first Brioullin zone (BZ) only or from the entire first BZ. For sufficiently high intensities of the driving laser field, we find relevant contributions to HHG from the entire first BZ. Here, based on numerically calculated spectra, we scrutinize the cutoff harmonic orders as a function of the laser peak intensity and find good qualitative agreement with our analytical saddle-point-approximation predictions and published theoretical data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1978

Theoretical study of collinear Be + FH/nu1/ yields BeF/nu2/ + H

The potential energy surface for collinear Be + FH yields BeF + H was studied at various levels of ab initio approximation. A final surface was obtained from a first order configuration interaction wave function, using the iterative orbital method and a medium-sized basis of Slater atomic functions. The exothermicity is computed to be 6 kcal/mole; the barrier height is predicted to be about 28 kcal/mole at a geometry where both internuclear separations are extended by about 0.4 bohr from their asymptotic equilibrium values. This surface differs qualitatively from simple LEPS models.

Schor, H.↗
DOE OSTI2014

CCHCR1 interacts with EDC4, suggesting its localization in P-bodies

Coiled‐coil alpha‐helical rod protein 1 (CCHCR1) is suggested as a candidate biomarker for psoriasis for more than a decade but its function remains poorly understood because of the inconsistent findings in the literature. CCHCR1 protein is suggested to be localized in the cytoplasm, nucleus, mitochondria, or centrosome and to regulate various cellular functions, including steroidogenesis, proliferation, differentiation, and cytoskeleton organization. In this study, we attempted to find a consensus between these findings by identifying the interaction partners of CCHCR1 using co-immunoprecipiation with a stable cell line expressing EGFP-tagged CCHCR1. Out of more than 100 co-immunoprecipitants identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), the enhancer of mRNA-decapping protein 4 (EDC4), which is a processing body (P-body) component, was particularly found to be the major interacting partner of CCHCR1. Confocal imaging confirmed the localization of CCHCR1 in P-bodies and its N-terminus is required for this subcellular localization, suggesting that CCHCR1 is a novel P-body component. As P-bodies are the site for mRNA metabolism, our findings provide a molecular basis for the function of CCHCR1, any disruption of which may affect the transcriptome of the cell, and causing abnormal cell functions. - Highlights: • We identified CCHCR1 as a novel P-body component. • We identified EDC4 as the major interacting partner of CCHCR1. • N-terminus of CCHCR1 protein is required for its P-bodies localization.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Description of electron transfer in the ground and excited states of organic donor–acceptor systems by single-reference and multi-reference density functional methods

Electron transfer in the ground and excited states of a model donor–acceptor (D–A) system is investigated using the single-reference and multi-reference density functional theory (DFT) methods. To analyze the results of the calculations, a simple two-site multi-reference model was derived that predicts a stepwise electron transfer in the S{sub 0} state and a wave-like dependence of the S{sub 1} electron transfer on the external stimulus. The standard single-reference Kohn-Sham (KS) DFT approach and the time-dependent DFT (TDDFT) method failed to describe the correct dependence of the S{sub 0} and S{sub 1} electron transfer on the external electric field applied along the donor–acceptor system. The multi-reference DFT approach, the spin-restricted ensemble-referenced KS (REKS) method, was able to successfully reproduce the correct behavior of the S{sub 0} and S{sub 1} electron transfer on the applied field. The REKS method was benchmarked against experimentally measured gas phase charge transfer excitations in a series of organic donor–acceptor complexes and displayed its ability to describe this type of electronic transitions with a very high accuracy, mean absolute error of 0.05 eV with the use of the standard range separated density functionals. On the basis of the calculations undertaken in this work, it is suggested that the non-adiabatic coupling between the S{sub 0} and S{sub 1} states may interfere with the electron transfer in a weakly coupled donor–acceptor system. It is also suggested that the electronic excitation of a D{sup +}–A{sup −} system may play a dual role by assisting the further electron transfer at certain magnitudes of the applied electric field and causing the backward transfer at lower electric field strengths.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Density functional theory investigation of the electronic structure and thermoelectric properties of layered MoS{sub 2}, MoSe{sub 2} and their mixed-layer compound

First principles density functional theory calculations were carried out for the 2H-MoQ{sub 2} (Q=S and Se) and their hypothetical mixed-layer compound. Due to the different electronegativities of S and Se atoms on MoQ{sub 2}, the band gap size could be adjusted in mixed-layer compound MoS{sub 2}/MoSe{sub 2}. Also, the indirect band gap in pure MoQ{sub 2} compounds is changed to the pseudo direct band gap in mixed-layer MoS{sub 2}/MoSe{sub 2} which is similar to the monolayer compound. The layer mixing enhances the thermoelectric properties because of the increased density of states around the Fermi level and the decreased band gap size. Therefore, we suggest that this layer mixing approach should be regarded as a useful way to modulate their electronic structures and to improve their thermoelectric properties. -- Graphical abstract: On the basis of density functional calculations we predict that the mixed-layer compounds 2H-MoS{sub 2}/2H-MoSe{sub 2}, in which two different layers 2H-MoS{sub 2} and 2H-MoSe{sub 2}, have enhanced thermoelectric properties because of the increased density of states around the Fermi level and the decreased band gap size. Highlights: • We explored a way of improving TE properties of 2H-MoQ{sub 2} on DFT methods. • The mixed-layer compounds MoS{sub 2}/MoSe{sub 2} have enhanced thermoelectric properties. • This is caused by modulated electronic structure of mixed layer compound. • Layer mixing approach should be regarded as a useful way to improve TE properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Giant magnetic anisotropy and tunnelling of the magnetization in Li2(Li1-xFex)N

Large magnetic anisotropy and coercivity are key properties of functional magnetic materials and are generally associated with rare earth elements. Here we show an extreme, uniaxial magnetic anisotropy and the emergence of magnetic hysteresis in Li2(Li 1-x Fe x )N. An extrapolated, magnetic anisotropy field of 220 T and a coercivity field of over 11 T at 2 K outperform all known hard ferromagnets and single-molecular magnets. Steps in the hysteresis loops and relaxation phenomena in striking similarity to single-molecular magnets are particularly pronounced for x<<1 and indicate the presence of nanoscale magnetic centres. Quantum tunnelling, in the form of temperature-independent relaxation and coercivity, deviation from Arrhenius behaviour and blocking of the relaxation, dominates the magnetic properties up to 10 K. The simple crystal structure, the availability of large single crystals and the ability to vary the Fe concentration make Li2(Li 1-x Fe x )N an ideal model system to study macroscopic quantum effects at elevated temperatures and also a basis for novel functional magnetic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Enhancing Electrophoretic Display Lifetime: Thiol-Polybutadiene Evaporation Barrier Property Response to Network Microstructure

An evaporation barrier is required to enhance the lifetime of electrophoretic deposition (EPD) displays. As EPD functions on the basis of reversible deposition and resuspension of colloids suspended in a solvent, evaporation of the solvent ultimately leads to device failure. Incorporation of a thiol-polybutadiene elastomer into EPD displays enabled display lifetime surpassing six months in counting and catalyzed rigid display transition into a flexible package. Final flexible display transition to mass production compels an electronic-ink approach to encapsulate display suspension within an elastomer shell. Final thiol-polybutadiene photosensitive resin network microstructure was idealized to be dense, homogeneous, and expose an elastic response to deformation. Research at hand details an approach to understanding microstructural change within display elastomers. Polybutadiene-based resin properties are modified via polymer chain structure, with and without added aromatic urethane methacrylate difunctionality, and in measuring network response to variation in thiol and initiator concentration. Dynamic mechanical analysis results signify that cross-linked segments within a difunctionalized polybutadiene network were on average eight times more elastically active than that of linked segments within a non-functionalized polybutadiene network. Difunctionalized polybutadiene samples also showed a 2.5 times greater maximum elastic modulus than non-functionalized samples. Hybrid polymer composed of both polybutadiene chains encompassed TE-2000 stiffness and B-1000 elasticity for use in encapsulating display suspension. Later experiments measured kinetic and rheological response due to alteration in dithiol cross-linker chain length via real time Fourier transform infrared spectroscopy and real-time dynamic rheology. Distinct differences were discovered between dithiol resin systems, as maximum thiol conversion achieved in short and long chain length dithiols was 86% and 11%, respectively. Oscillatory real-time rheological experiments confirmed a more uniform network to better dissipate applied shear in short chain length dithiol systems, as long chain length dithiols relayed a steep internal stress build-up due to less cross-links and chain entanglements. Thorough understanding of network formation aids the production of a stronger and impermeable elastomeric barrier for preservation of EPD displays.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Electric field enhancement in a self-assembled 2D array of silver nanospheres

We investigate the plasmonic properties of a self-assembled 2D array of Ag nanospheres (average particle diameter/inter-particle separation distance of 9/3.7 nm). The structures of the individual particles and their assemblies are characterized using high-resolution transmission electron microscopy (HR-TEM). The plasmonic response of the nanoparticle network is probed using two-photon photoemission electron microscopy (TP-PEEM). HR-TEM and TP-PEEM statistics reveal the structure and plasmonic response of the network to be homogeneous on average. This translates into a relatively uniform surface-enhanced Raman scattering (SERS) response from biphenyl,4-4{sup ′}-dithiol (BPDT) molecules adsorbed onto different sites of the network. Reproducible, bright, and low-background SERS spectra are recorded and assigned on the basis of density functional theory calculations in which BPDT is chemisorbed onto the vertex of a finite tetrahedral Ag cluster consisting of 20 Ag atoms. A notable agreement between experiment and theory allows us to rigorously account for the observable vibrational states of BPDT in the ∼200–2200 cm{sup −1} region of the spectrum. Finite difference time domain simulations further reveal that physical enhancement factors on the order of 10{sup 6} are attainable at the nanogaps formed between the silver nanospheres in the 2D array. Combined with modest chemical enhancement factors, this study paves the way for reproducible single molecule signals from an easily self-assembled SERS substrate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗